QDESCP

class qdescp(**kwargs)

Class containing all the functions from the QDESCP module related to xTB properties for SDF files.

collect_xtb_properties()

Collects all xTB properties from the files and puts them in a JSON file

run_sp_xtb(xyz_file, charge, mult, name, destination)

Runs single point xTB calculations to collect properties

Parameters

General

w_dir_mainstr, default=os.getcwd()

Working directory

destinationstr, default=None,

Directory to create the JSON file(s)

programstr, default=None

Program required to create the new descriptors. Current options: 'xtb', 'nmr'

XTB descriptors

fileslist of str, default=''

Filenames of SDF/PDB/XYZ files to calculate xTB descriptors. If *.sdf (or other strings that are not lists such as *.pdb) are specified, the program will look for all the SDF files in the working directory through glob.glob(*.sdf)

chargeint, default=None

Charge of the calculations used in the following input files (charges from SDF files generated in CSEARCH are read automatically).

multint, default=None

Multiplicity of the calculations used in the following input files (multiplicities from SDF files generated in CSEARCH are read automatically).

qdescp_solventstr, default=None

Solvent used in the xTB property calculations (ALPB model)

qdescp_tempfloat, default=300

Temperature required for the xTB property calculations

qdescp_accfloat, default=0.2

Accuracy required for the xTB property calculations

boltzbool, default=False

Calculation of Boltzmann averaged xTB properties and addition of RDKit molecular descriptors

NMR simulation

fileslist of str, default=''

Filenames of LOG files to retrieve NMR shifts from Gaussian calculations (*.log can be used to include all the log files in the working directory)

boltzbool, default=False

Calculation of Boltzmann averaged NMR shifts

nmr_atomslist of str, default=[6, 1]

List containing the atom types (as atomic numbers) to consider. For example, if the user wants to retrieve NMR shifts from C and H atoms nmr_atoms=[6, 1]

nmr_slopelist of float, default=[-1.0537, -1.0784]

List containing the slope to apply for the raw NMR shifts calculated with Gaussian. A slope needs to be provided for each atom type in the analysis (i.e., for C and H atoms, the nmr_slope=[-1.0537, -1.0784]). These values can be adjusted using the CHESHIRE repository.

nmr_interceptlist of float, default=[181.7815, 31.8723]

List containing the intercept to apply for the raw NMR shifts calculated with Gaussian. An intercept needs to be provided for each atom type in the analysis (i.e., for C and H atoms, the nmr_intercept=[-1.0537, -1.0784]). These values can be adjusted using the CHESHIRE repository.

nmr_experimstr, default=None

Filename of a CSV containing the experimental NMR shifts. Two columnds are needed: A) 'atom_idx' should contain the indexes of the atoms to study as seen in GaussView or other molecular visualizers (i.e., the first atom of the coordinates has index 1); B) 'experimental_ppm' should contain the experimental NMR shifts in ppm observed for the atoms.